NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1169100938|ref|NP_001336776|]
View 

DNA topoisomerase 3-beta-1 isoform 1 [Homo sapiens]

Protein Classification

DNA topoisomerase III( domain architecture ID 10129755)

topoisomerase III is a type 1a topoisomerase that resolves single strand DNA recombination and replication intermediates

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


:

Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1169100938 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


:

Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362     1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362    72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                  ....*.
gi 1169100938 162 NAMACL 167
Cdd:cd03362   146 RAFKNL 151
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1169100938 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-752 4.73e-146

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 451.38  E-value: 4.73e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLS--SHKGLNgacsVHEytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219    1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahgGEKTVFRARFSSITDTDI 160
Cdd:PRK07219   73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 161 CNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219  144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 241 WVLQAKVNTD---KDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMG 317
Cdd:PRK07219  221 WKIEALLDKEaqyFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGIS 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 318 PQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK07219  301 PKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVP 380

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 397 TEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSvPLEESLPTCQRGDAF 476
Cdd:PRK07219  381 KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKL 459

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 477 PVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveSGRRLKPTNLGIVLVHGYYKIDAELV 556
Cdd:PRK07219  460 KVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIV 537

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 557 LPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQ 635
Cdd:PRK07219  538 SEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIR 616

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 636 AKPSR--LHCS---HCDETYTLPQNGTIKL--------------------YKELRCPLDDFELvlwSSGSRGKSYPLCPY 690
Cdd:PRK07219  617 TDKGSrfVGCSgypDCRNTFPLPSTGRIKVldevcekcglpvikilrgkqTFVVGCPDCEAEK---EEEDPDEVIGPCPK 693

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1169100938 691 CYNHPPFRDMKKG--MGCNEctHPSCQHSLSM-------LGIGQCVECESGVLVLDPTSGPKWKVACN-KCN 752
Cdd:PRK07219  694 CGGELAIKQLKYGsfLGCTN--YPKCKYTLPLprrgkitVTDEKCPECGLPLLRVKGGFGDELGCCNNpKCN 763
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 5.96e-140

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 421.27  E-value: 5.96e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVN 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 249 TDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEK-EAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADTVKRLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 1169100938 564 VEKQLNLIAQGKADYRQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 3.73e-105

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 324.97  E-value: 3.73e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  290 RKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADTVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  369 RLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCS 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  444 GKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 1169100938  524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 3.45e-94

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 306.25  E-value: 3.45e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   5 LMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550     3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  85 APT----EKKEanPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARFSSITDTDI 160
Cdd:COG0550    49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 161 CNAMACLGEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550   116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 238 ETYWVLQAKVNTDKD--RSLLLDWDRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLG 315
Cdd:COG0550   185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 316 MGPQHAMQTAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADTVKRLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550   264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEE----SLPT 469
Cdd:COG0550   338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 470 CQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550   418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1169100938 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYRQVLGHtldvFKRKFH 594
Cdd:COG0550   494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362     1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362    72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                  ....*.
gi 1169100938 162 NAMACL 167
Cdd:cd03362   146 RAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 1.42e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 58.52  E-value: 1.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   4 VLMVAEKPSLAQSIAKILSRGSlsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1169100938  84 qaptekkeaNPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahggEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 1.04e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938    4 VLMVAEKPSLAQSIAKILSRgslsshkglngacsvheytgtfagqpvRFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1169100938   84 qaptekkeanpklnMVKFLQVEGRGCdYIVLWLDCDKEGENICFEVLDAVLPVM 137
Cdd:smart00493  37 --------------QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Name Accession Description Interval E-value
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 172-593 1.51e-150

DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.


Pssm-ID: 238110 [Multi-domain]  Cd Length: 381  Bit Score: 447.44  E-value: 1.51e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 172 HNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQakvntdk 251
Cdd:cd00186     1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 252 drsllldwdrvrvfdreiaqmflnmtklekEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331
Cdd:cd00186    68 ------------------------------EAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEA 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAeGINRPRKGHDAGDHPPITPMK----SATEAELGGDAWR 407
Cdd:cd00186   118 GLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLG-RRNPKRGKKEQGAHEAIRPTKvaptPELEANLSEDEFK 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 408 LYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:cd00186   197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567
Cdd:cd00186   277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE-KKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355

                         410       420
                  ....*....|....*....|....*.
gi 1169100938 568 LNLIAQGKADYRQVLGHTLDVFKRKF 593
Cdd:cd00186   356 LDEIAEGKKDYQEVLEEFYEEFKKIV 381
PRK07219 PRK07219
DNA topoisomerase I; Validated
 3-752 4.73e-146

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 451.38  E-value: 4.73e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLS--SHKGLNgacsVHEytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE 80
Cdd:PRK07219    1 TELIIAEKNNAARRIADILSGGKAKkkRVNGVP----YYE----FERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  81 LFSqAPTEKKEANPklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahgGEKTVFRARFSSITDTDI 160
Cdd:PRK07219   73 LID-ADPVKKITKQ--NYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV------CQVPVKRARFSSLTKKEI 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 161 CNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFqGKYGDLDssLISFGPCQTPTLGFCVERHDKIQSFKPETY 240
Cdd:PRK07219  144 RKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSV-RQLGRWD--FLSVGRVQTPTLAFIVDREREIRAFDPEDY 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 241 WVLQAKVNTD---KDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMG 317
Cdd:PRK07219  221 WKIEALLDKEaqyFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGIS 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 318 PQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK07219  301 PKRAMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGkKETTDHPPIHPVDVP 380

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 397 TEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSvPLEESLPTCQRGDAF 476
Cdd:PRK07219  381 KREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEK-FDEKELPDLEEGEKL 459

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 477 PVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTveSGRRLKPTNLGIVLVHGYYKIDAELV 556
Cdd:PRK07219  460 KVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVI--EGDPPRPTDLGIAVIEALEKYAPEIV 537

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 557 LPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELMEvSFSPLAATGKPLSRCGKCHRFMKYIQ 635
Cdd:PRK07219  538 SEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgDHLAG-SLKAENRSLKTIGKCPECGGDLIIIR 616

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 636 AKPSR--LHCS---HCDETYTLPQNGTIKL--------------------YKELRCPLDDFELvlwSSGSRGKSYPLCPY 690
Cdd:PRK07219  617 TDKGSrfVGCSgypDCRNTFPLPSTGRIKVldevcekcglpvikilrgkqTFVVGCPDCEAEK---EEEDPDEVIGPCPK 693

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1169100938 691 CYNHPPFRDMKKG--MGCNEctHPSCQHSLSM-------LGIGQCVECESGVLVLDPTSGPKWKVACN-KCN 752
Cdd:PRK07219  694 CGGELAIKQLKYGsfLGCTN--YPKCKYTLPLprrgkitVTDEKCPECGLPLLRVKGGFGDELGCCNNpKCN 763
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 169-582 5.96e-140

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 421.27  E-value: 5.96e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 169 EPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKygdldsSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVN 248
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKGN------KLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 249 TDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEK-EAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAER 327
Cdd:pfam01131  75 DGGGVFANAKWKRGRIFDKEEAEAILE--KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 328 LYTQ-GYISYPRTETTHYPENFDLKGSLR-QQANHPYWADTVKRLLAEG-INRPRKGHDAGDHPPITPMKSAT-EAELGG 403
Cdd:pfam01131 153 LYEKhGLITYPRTDSTYLSDDATLKAILEyLTKNYGKYLPYAPRLLKKTkGKLTVGNAKVTAHEAIRPTGDIPvLPELSD 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVTQVEV 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDaELVLPTIRSA 563
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVERK-KKSLVPTELGKALVEALEKFP-DLVDPELTAE 390

                         410
                  ....*....|....*....
gi 1169100938 564 VEKQLNLIAQGKADYRQVL 582
Cdd:pfam01131 391 LEEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 290-544 3.73e-105

Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit


Pssm-ID: 214663 [Multi-domain]  Cd Length: 259  Bit Score: 324.97  E-value: 3.73e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  290 RKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHP-YWADTVK 368
Cdd:smart00437   2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGkEYLDLAV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  369 RLLAEGInrPRKGHDA-GDHPPITPMKSAT----EAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCS 443
Cdd:smart00437  82 VLLKPRK--PRKGKKAqGAHEAIRPTKPIFtpelEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAK 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  444 GKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQ 523
Cdd:smart00437 160 GKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239

                          250       260
                   ....*....|....*....|.
gi 1169100938  524 RNYVTVEsGRRLKPTNLGIVL 544
Cdd:smart00437 240 RGYVTKK-KKKLIPTELGIAV 259
PRK07220 PRK07220
DNA topoisomerase I; Validated
 5-658 2.02e-101

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 331.34  E-value: 2.02e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   5 LMVAEKPSLAQSIAKILSRGSLSSHKglngACSVHEYTGTFAGQpvRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFsQ 84
Cdd:PRK07220    3 LIITEKNIAARRIAQILAPKKPKKTR----VSGVDVYRYEDNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDARDLI-D 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  85 APTEKKEANPKLnmVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHggektVFRARFSSITDTDICNAM 164
Cdd:PRK07220   76 AEIITTPTQKKI--VTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVNPDIK-----FDRVRYSAITKKEIERAF 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 165 ACLGEPDHNEALSVDARQELDLRIGCAFTRfqtkYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQ 244
Cdd:PRK07220  149 SNPVEVDFNLADAGHSRQVIDLVWGAALTR----YISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIY 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 245 AKVnTDKDRSLLLDWDRVRVFDREIAQMFLNmtKLEKEAQVEATSRKEKAKQRPLALNTVEMLRvASSSLGMGPQHAMQT 324
Cdd:PRK07220  225 ATL-ENNGETFVAQHSTRRFWEKEEADRVFE--KLGKTAEVTEVEKGTKTDKPPTPFNTTEFIS-AANSIGFSAANAMRI 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 325 AERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYwADTVKRLLAEGINRPRKG-HDAGDHPPITPMKSATEAELGG 403
Cdd:PRK07220  301 AESLYTNGYISYPRTDNTVYPESLDLREQIEIFAEGPF-GEYAQKLLEKGELVPTRGkKETTDHPPIYPASLAKKSELKE 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 404 DAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQRGDAFPVGEVKM 483
Cdd:PRK07220  380 DEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPY-NAPEDRLLPELSEGEELKVKKKEM 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 484 LEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSA 563
Cdd:PRK07220  459 LDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---HGNPIQPTNTAFAVVDALEKYAPTITKPDMTSR 535

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 564 VEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSiagMDELMEVSFSPLAATgKPLSRCGKC-HRFMKYIQAKPSR-L 641
Cdd:PRK07220  536 LEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKN---REKIRESLREGLRED-KIIGKCPLCgSDLMVRRSKRGSRfI 611

                         650       660
                  ....*....|....*....|
gi 1169100938 642 HCS---HCDETYTLPQNGTI 658
Cdd:PRK07220  612 GCEgypECTFSLPLPKSGQI 631
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-594 3.45e-94

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 306.25  E-value: 3.45e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   5 LMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAELFsq 84
Cdd:COG0550     3 LVIVESPAKAKTIAKYLGKD---------------------------YVVTASVGHLRDL-----PKPELDVDVENDF-- 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  85 APT----EKKEanPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARFSSITDTDI 160
Cdd:COG0550    49 EPKyeviPGKK--KQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELL--------GDKKPVKRVVFNEITKKAI 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 161 CNAMACLGEPDHNeaLsVDA---RQELDLRIGCAFTRFQTKYFQGKygdldsslISFGPCQTPTLGFCVERHDKIQSFKP 237
Cdd:COG0550   116 KEAFKNPRDIDMN--L-VDAqqaRRILDRLVGYNLSPLLWKKVKRG--------LSAGRVQSPALRLIVEREREIEAFVP 184

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 238 ETYWVLQAKVNTDKD--RSLLLDWDRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLG 315
Cdd:COG0550   185 EEYWTIEATFKTGGGefTAKLVKIDGKKILDEEEAEAILAALK-GKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLG 263

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 316 MGPQHAMQTAERLYTQGYISYPRTETTHYPEnfDLKGSLRQQANhpywADTVKRLLAEGINRPRKGHDA-GDHPPITP-M 393
Cdd:COG0550   264 FSAKKTMSIAQRLYEVGLITYMRTDSVRLSE--DAVAAAREYIE----ALYGKEYLPEKPRVYKTSKNAqEAHEAIRPtG 337

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 394 KSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEE----SLPT 469
Cdd:COG0550   338 VTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEEeeekRLPP 417

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 470 CQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLGIV--- 543
Cdd:COG0550   418 LKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGrpsTYASI---IETLQDRGYVERE-GKRLVPTELGFIvid 493

                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1169100938 544 LVHGYYKidaELVLPTIRSAVEKQLNLIAQGKADYRQVLGHtldvFKRKFH 594
Cdd:COG0550   494 LLEEHFP---DLVDYEFTAKMEEKLDEIAEGKLDWKDVLEE----FYKPFK 537
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 5-621 6.90e-80

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 277.50  E-value: 6.90e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   5 LMVAEKPSLAQSIAKILSRGSLSSHKGlNGACSVHEYTGTFAgqpvrfkmTSVCGHVMTLDFLGKYNKWDKVD--PAELF 82
Cdd:PRK14973    3 LIIAEKNIAANRIAQILAGKTKVQVKK-DGGVSTYSFDDTVV--------VGLRGHVVEVDFEPGYTNWRSEEhtPRSLI 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  83 S----QAPTEKKeanpklnMVKFLQVEGRGCDYIVLWLDCDKEGENI---CFEVLDAVLPvmnkahggEKTVFRARFSSI 155
Cdd:PRK14973   74 DadtiKKPTEKK-------IVGLIQKLAKKADRVTIATDFDTEGELIgkeAYELVRAVNP--------KVPIDRARFSAI 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 156 TDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTkyFQGKYGDldSSLISFGPCQTPTLGFCVERHDKIQSF 235
Cdd:PRK14973  139 TKEEIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPTLAMIVDREKEIEAF 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 236 KPETYWVLQakVNTDKD-RSLLLDWDRVRVFDREIAQMFLNMTKlekeAQVEATSRKEKAKQ--RPLALNTVEMLrVASS 312
Cdd:PRK14973  215 VPEKYWMLS--LATEKDgEGIEARHTHGRFTDSAAAEAAYDATK----EPLVVTEVKEGHKVdrAPTPFDTTTFI-VAAS 287

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 313 SLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADtVKRLLAEGINRPRKGH-DAGDHPPIT 391
Cdd:PRK14973  288 RLGFSAANAMRIAEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKGAFSKD-VAWVKDNRRPVPTRGKkSSTDHPPIH 366

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQ 471
Cdd:PRK14973  367 PTGVATREELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPY-SEAKENILPAFA 445

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 472 RGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVtveSGRRLKPTNLGIVLVHGYYKI 551
Cdd:PRK14973  446 LGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---EGNPLRPTLVGRAVTESLEEH 522

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1169100938 552 DAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGM-DELM-----EVSFSPLAATGKPL 621
Cdd:PRK14973  523 AGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMertaeELTIGPCPVCGKDL 598
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 4-629 3.55e-61

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 219.86  E-value: 3.55e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   4 VLMVAEKPSLAQSIAKILSRGSLSSHKGlngacSVHEYTGTFAGQpvRFKMTSVCGHVMTLDFLGK-YNKWDkVDPAELF 82
Cdd:PRK05776    3 ILVIAEKPKAARKIAEALSEKPIRCRIY-----GVPYWIVKRDGK--KIVVAPAAGHLFGLHTKSKgFPVFD-YEWKPLY 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  83 sQAPTEKKEANPKLNMVKFLqveGRGCDYIVLWLDCDKEGENICFEVLdavlpvmnKAHGGEKTVFRARFSSITDTDICN 162
Cdd:PRK05776   75 -EIDKGSKYTKKYYELLSSL---SKYADEFINACDYDIEGSVIGYLII--------KYLGDPKKAKRMKFSALTKSDIRR 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 163 AMACLGEPDHNEALSVDARQELDLRIGCAFTRFQT---KYFQGKygdldSSLISFGPCQTPTLGFCVERHDKIQSFKPET 239
Cdd:PRK05776  143 AFRNLETLDYEMINAGIARHELDWLWGINVSRALMssvRDASGK-----RVILSAGRVQSPTLKYVVEREIERNLFVPLP 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 240 YWVLQAKVNTdKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQ 319
Cdd:PRK05776  218 YFSVSIIIEK-NGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPY 296

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 320 HAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAE--GINRPRKG-HDAGDHPPITPMKSA 396
Cdd:PRK05776  297 KTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKEtkGVLKPVQGpKDDPAHPAIYPTGEP 376

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 397 TEaELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIG--PELFTCSGKTVLSPGFTEVMPWqSVPLEESLPTCQRGD 474
Cdd:PRK05776  377 PK-NLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPgfPLVFSASGQRIEERGWLKYYPF-HKFDEEELPLLKKGE 454

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 475 AFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTvESGRRLKPTNLGIVLVHGYYKIDAE 554
Cdd:PRK05776  455 RVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SNGKYIEVTPLGFGVAEVLEKYFPD 533

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 555 LVLPTIRSAVEKQLNLIAQGKADYRQVLGHT-------LDVFKRKFHYFVDSIAGMDELMevsfsplaatgKPLSRCGKC 627
Cdd:PRK05776  534 IVSVELTRDFEEKLEMIRTGKATREEVIEEAketlnklLEEFKKNKDEIGEELAKALGLI-----------KPVGKCKIC 602


                  ..
gi 1169100938 628 HR 629
Cdd:PRK05776  603 GR 604
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
 3-167 2.83e-54

TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173782 [Multi-domain]  Cd Length: 151  Bit Score: 184.74  E-value: 2.83e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGacsvheytgTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAE-L 81
Cdd:cd03362     1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYY---------EFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEdP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  82 FSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNkahggeKTVFRARFSSITDTDIC 161
Cdd:cd03362    72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKR------KPVKRAWFSSLTPKAIR 145


                  ....*.
gi 1169100938 162 NAMACL 167
Cdd:cd03362   146 RAFKNL 151
PRK07726 PRK07726
DNA topoisomerase 3;
1-646 3.36e-51

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 190.76  E-value: 3.36e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTVLmvAEKPSLAQSIAKILSrgslsSHKGLNGACSVHEYTGTFAgqpvrfkmtsvCGHVMTL----DFLGKYNKWDKV 76
Cdd:PRK07726    1 MRLFI--AEKPSVGRDIADVLK-----PHKKGDGYIEGNGYIVTWA-----------IGHLLELaepeAYDERYKRWRLE 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  77 D----PAELFSQApteKKEANPKLNMVKFL--QVegrgcDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRA 150
Cdd:PRK07726   63 DlpiiPEKWKLVV---KKKTAKQFNVVKKLlkQA-----TEIVIATDADREGELIAREILDYC--------GVRKPIKRL 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 151 RFSSITDTDICNAMACL--G---EPDHNEALsvdARQELDLRIGCAFTR-FQTKYFQGKYGDLdsslISFGPCQTPTLGF 224
Cdd:PRK07726  127 WISSLTDKAIKRAFANLkpGketIPLYYSAL---ARSRADWLVGINMTRaYTLLGRKAGYNGV----LSVGRVQTPTLAL 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 225 CVERHDKIQSFKPETYWVLQAKVNTDKDRSLLldW--------DRVRVFDREIAQMFLNMTKlEKEAQVEATSRKEKAKQ 296
Cdd:PRK07726  200 VVRRDEEIENFVPKPYWEVEAHLTPGERFTAK--WqpsepyqdEEGRLLDRPLAEQVVARIQ-GQPAKVTEVETKRKKEY 276

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 297 RPLALNTVEMLRVASSSLGMGPQHAMQTAERLY-TQGYISYPRTETTHYPEnfDLKGSLRQ-----QANHPYwadtvKRL 370
Cdd:PRK07726  277 APLLYDLSELQIDANKRFGLSAKETLDIAQSLYeTHKLITYPRTDSRYLPE--DMVATLPEvlnaiSKVDPY-----LLL 349

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 371 LAEGINRPRKGH---DA--GDHPPITP-MKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSG 444
Cdd:PRK07726  350 APPVLDPSIRSRawnDKkvTAHHAIIPtEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKG 429

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 445 KTVLSPGFTEVMPWQSVPLEES--LPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLM-----------------EK 505
Cdd:PRK07726  430 KQVVEAGWKALLGKKEEDEEKEqpLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMeniarfvqdkelkktlkET 509

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 506 HGIGTDA---SIpvhINNICQRNYVTVEsGRRLKPTNLGIVLvhgyykIDA---ELVLPTIRSAVEKQLNLIAQGKADYR 579
Cdd:PRK07726  510 DGLGTEAtraGI---IEKLFKRGYLEKK-GKYIHATDKGKQL------IDAlpeELTSPDMTAKWEQALDQISEGQLSYQ 579

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1169100938 580 QvlghtldvfkrkfhyFVDSIAG-MDELME---VSFSPLAATGKPLSRCGKCHRFMKyiQAKPSRLHCSHC 646
Cdd:PRK07726  580 D---------------FMQPLKQwLKQLVEqakQSSEKYKFDNLTGPKCPDCGKPML--KVKGKNGKMLVC 633
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 3-167 2.94e-44

TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173778 [Multi-domain]  Cd Length: 142  Bit Score: 156.23  E-value: 2.94e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   3 TVLMVAEKPSLAQSIAKILSRGSLSSHkglngacsvheytgtFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELF 82
Cdd:cd01028     1 KVLIIAEKPSKAKTIAKILGKGSKKKG---------------FYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELF 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  83 sQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPvmnkahgGEKTVFRARFSSITDTDICN 162
Cdd:cd01028    66 -PFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-------DNKPVKRAWFSEITPKAIRE 137


                  ....*
gi 1169100938 163 AMACL 167
Cdd:cd01028   138 AFKNL 142
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-688 2.40e-37

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 149.62  E-value: 2.40e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDflgkyNKWDKVDPAE 80
Cdd:PRK06599    1 MAKKLVIVESPAKAKTIKKYLGKD---------------------------YKVLASFGHVRDLP-----KKKGGVDPDN 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  81 LFsqAPT----EKKEanpklNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDavlpVMNKAHGGEKTVFRARFSSIT 156
Cdd:PRK06599   49 DF--APKyeiiEGKE-----KVVDALKKAAKKADAVYLATDPDREGEAIAWHIAE----VLKEAKLKDKNVKRVVFNEIT 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 157 DTDICNAMAclgEP-DHNEALsVD---ARQELDLRIGcaftrFQ------TKYFQGKygdldssliSFGPCQTPTLGFCV 226
Cdd:PRK06599  118 KKAVQEAIE---NPrDIDMDL-VDaqqARRALDYLVG-----FKlspllwKKVRRGL---------SAGRVQSVALRLIC 179

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 227 ERHDKIQSFKPETYWVLQAKVNTDKDRSL---LLDWD-----RVRVFDREIAQmflnmtKLEKEAQ-----VEATSRKEK 293
Cdd:PRK06599  180 EREDEIEAFIPQEYWTIEADLATSNGEPFtakLVEVNgkkleKFSITNEEQAK------ALVKALEgqaytVDKIEKKER 253

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 294 AKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLY--------TQGYISYPRTETThypenfdlkgslrqqanhpywad 365
Cdd:PRK06599  254 KRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYegidlgegTVGLITYMRTDSV----------------------- 310

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 366 tvkRLLAEGINRPRK------GHD-AGDHPPI--TPMKSATEAE------------------LGGDAWRLYEYITRHFIA 418
Cdd:PRK06599  311 ---RLSNEALDEARKyitkkyGKEyLPAKPRVykKKSKNAQEAHeairptsinrtpeslkpyLTPDQFKLYELIWKRTVA 387

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 419 TVSHDCKYLQSTISF--RIGPELFTCSGKTVLSPGFTEVMPwQSVPLEES-----LPTCQRGDAFPVGEVkmLEKQ--TN 489
Cdd:PRK06599  388 SQMAPAILDQTSVDIasENGKYVFRATGSVILFPGFLKVYG-ESKDDEEEddeklLPPLKEGEKLKLDEL--LPEQhfTE 464

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 490 PPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLG-IV---LVHGY-----YKIDAELvl 557
Cdd:PRK06599  465 PPPRYSEASLVKKLEEYGIGrpsTYASI---ISTLQDREYVELE-KKRFIPTDLGrIVndfLVEHFpkyvdYDFTAGL-- 538

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 558 ptirsavEKQLNLIAQGKADYRQVlghtLDVFKRKFHYFVDSIAGMDELMEVSFSPLAAT-----GKPLS-RCGKCHRFm 631
Cdd:PRK06599  539 -------EDELDEIAEGKKDWKPV----LREFWEPFISNLEKVEEDVRTEKVTQEETDETcpkcgGGPLVlKLGKNGKF- 606

                         730       740       750       760       770       780       790
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 632 kyiqakpsrLHCSH---CDETYTLPQNG-----TIKLYKELRCPLDDFELVLwSSGSRGK-----SYPLC 688
Cdd:PRK06599  607 ---------LGCSGypeCKYTKNITRDEdepieEEEIVEEEKCPKCGGPLVL-KKGRYGKflacsGYPEC 666
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 108-631 1.26e-36

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 148.79  E-value: 1.26e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 108 GCDYIVLWLDCDKEGENICFEVLDaVLpvmnkaHGGEKTVFRARFSSITDTDICNAMAclgEP-DHNEALsVDA---RQE 183
Cdd:PRK07561   86 DADELYLATDPDREGEAIAWHLLE-VL------GGDDVPVKRVVFNEITKNAIQEAFE---NPrELDINL-VNAqqaRRF 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 184 LDlRIgcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSL 255
Cdd:PRK07561  155 LD-RL---------------VGYMVSPLLwkkiarglSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAF 218

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 256 LLD--------WDRVRVFDREIAQMFLnmTKLEKeAQVEATSRKEKAKQR-PLALNTVEMLRVASSS-LGMGPQHAMQTA 325
Cdd:PRK07561  219 EARlthldgkkFAPVDLLNEAQAEAAV--AALEG-ARYSVASVEDKPTTRkPSAPFTTSTLQQEASRkLGFSVKKTMRIA 295

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 326 ERLYTQGYISYPRTETTHY-PENFDlkgSLRQQANHPYWADtvkrLLAEGinrPR------KG----HDAgdhppITP-- 392
Cdd:PRK07561  296 QRLYEAGYITYMRTDSTNLsQEAIN---AARGYIGDNYGKK----YLPEK---PRqysskaKNaqeaHEA-----IRPsd 360

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 393 -MKSATE-AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQS--VPLEES-- 466
Cdd:PRK07561  361 vFRTPDQlKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRddALDDEDrr 440

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 467 LPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDASIpvhINNICQRNYVTVEsGRRLKPTNLG-I 542
Cdd:PRK07561  441 LPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGrpsTYASI---ISTIQDRGYVRLE-NRRFYPEKMGrI 516

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 543 V--LVHGYYkidAELVLPTIRSAVEKQLNLIAQGKADYRQVlghtLDVFKRKFHYFVDSIA------GMDELMEVsfspl 614
Cdd:PRK07561  517 VtdRLEEFF---PRLVDYDFTARMEEELDDIANGEADWKPV----LDDFYKDFSQQLEKAEelreegGMRPNQMV----- 584

                         570
                  ....*....|....*...
gi 1169100938 615 aatgkPLSR-CGKCHRFM 631
Cdd:PRK07561  585 -----ITDRdCPTCGRGM 597
PRK08173 PRK08173
DNA topoisomerase III; Validated
 1-647 6.97e-34

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 140.19  E-value: 6.97e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTVLMVAEKPSLAQSIAKILsrGSLSSHKglngacsvhEYtgtFAGQpvRFKMTSVCGHVMTL----DFLGKYNKWD-- 74
Cdd:PRK08173    1 MSKALIIAEKPSVANDIARAL--GGFTKHD---------EY---FESD--EYVLSSAVGHLLEIaapeEYEVKRGKWSfa 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  75 --KVDPaELFSQAPTEKKEANPKLnMVKflQVEGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnkahGGEKTVFRARF 152
Cdd:PRK08173   65 hlPVIP-PHFDLNPIAKTESRLKV-LTK--LIKRKDVTRLINACDAGREGELIFRLIAQHA--------KAKKPVKRLWL 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 153 SSITDTDICNAMACLGEPDHNEALSvDA---RQELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVERH 229
Cdd:PRK08173  133 QSMTPQAIRDGFANLRSDEDMQPLA-DAarcRSEADWLVGINGTRAMTA-FNSKGGGF--FLTTVGRVQTPTLSIVVERE 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 230 DKIQSFKPETYWVLQA-------------------KVNTDKDRsllldwdRV-RVFDREIAQMFLNMTKlEKEAQVEATS 289
Cdd:PRK08173  209 EKIRRFVPRDYWEVRAefvaaagfyegrwfdpkfkKDEFDPEK-------RAsRLWSEAAAEAIVAACR-GKPGTVTEES 280

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 290 rKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ-GYISYPRTETTHYPENF--DLKGSLRQQANHPYWADT 366
Cdd:PRK08173  281 -KPSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYlgTVKQTLEMLKESNNYLPH 359

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 367 VKRLLAEGINRPRK----GHDAGDHPPITPM----KSATEAELggdawRLYEYITRHFIATVSHDCKYLQSTISFRIGPE 438
Cdd:PRK08173  360 AKQILDKGWVKPNKrifdNSKISDHFAIIPTlqapKSLSEPEQ-----KLYDLVVKRFLAVFFPAAEFLVTTRITEVAGH 434

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 439 LFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLME-------------- 504
Cdd:PRK08173  435 HFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklveddelrea 514

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 505 --KHGIGTDASIPVHINNICQRNYVtVESGRRLKPT----NLgIVLVHGyYKIDaELVLPTIRSAVEKQLNLIAQGK--- 575
Cdd:PRK08173  515 maEKGLGTPATRAAIIEGLLGEKYL-VREGRELIPTakafQL-MTLLRG-LGVE-ELTSPELTGEWEYKLSQIERGKlsr 590

                         650       660       670       680       690       700       710
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1169100938 576 -ADYRQVLGHTLDVFKRKFHYFVDSIAGmdelmevSFSPLAAtgkPLSRCGkchrfmKYIQAKPSRLHCSHCD 647
Cdd:PRK08173  591 dAFMQEIAQMTQQIVKRAKEYDSDTIPG-------DYATLQT---PCPNCG------GVVKENYRRFACTKCD 647
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 147-242 1.10e-32

Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit


Pssm-ID: 214662 [Multi-domain]  Cd Length: 89  Bit Score: 121.54  E-value: 1.10e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  147 VFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYgdldsslISFGPCQTPTLGFCV 226
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNGV-------LSAGRVQTPTLGLIV 73

                           90
                   ....*....|....*.
gi 1169100938  227 ERHDKIQSFKPETYWV 242
Cdd:smart00436  74 EREREIKNFVPKPYWE 89
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 1-635 3.80e-31

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 131.04  E-value: 3.80e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLdflgkYNKWDKVDPAE 80
Cdd:PRK08780    1 MSKHLVIVESPAKAKTINKYLGKD---------------------------FTVLASYGHVRDL-----VPKEGAVDPEN 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  81 LFSQ--APTEKKEANpklnmVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVlpvmnKAHG--GEKTVFRARFSSIT 156
Cdd:PRK08780   49 GFAMryDLIDKNEKH-----VEAIAKAAKSADDLYLATDPDREGEAISWHLAEIL-----KERGllKDKPMQRVVFTEIT 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 157 DTDICNAMAclgepdHNEALSVD------ARQELDLRIGCAFTRFQTKYFQgkygdldsSLISFGPCQTPTLGFCVERHD 230
Cdd:PRK08780  119 PRAIKEAMA------KPRDIASDlvdaqqARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVEREE 184

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 231 KIQSFKPETYWVLQAKVNTDKD----RSLLLDWDRVRVF---DREIAQMFLNmtKLEKEAQ----VEATSRKEKaKQRPL 299
Cdd:PRK08780  185 EIEAFIAREYWSIEADCAHPSQpfnaKLIKLDGQKFEQFtitDGDTAEAARL--RIQQAAQgtlhVTDVESKER-KRNPA 261

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 300 ALNTVEMLRV-ASSSLGMGPQHAMQTAERLY---------TQGYISYPRTETTHYPEnfDLKGSLRQQANHPYWADTVKR 369
Cdd:PRK08780  262 PPFTTSTLQQeASRKLGFTTRRTMQVAQKLYegvdlgdegSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLPD 339

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 370 LLAEGINRPRKGHDAgdHPPITP---MKSATE--AELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPE-LFTCS 443
Cdd:PRK08780  340 QPNTYKTKSKNAQEA--HEAVRPtsaLRTPAQvaRFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEhVFRAT 417

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 444 GKTVLSPGFTEVM-------PWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIG---TDAS 513
Cdd:PRK08780  418 GSTVVVPGFLAVYeegkddkSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGrpsTYAS 497

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 514 IpvhINNICQRNYVTVEsGRRLKPTNLGIVlVHGY----------YKIDAELvlptirsavEKQLNLIAQGKADYRQVLG 583
Cdd:PRK08780  498 I---ISTLQFRKYVEME-GRRFRPTDVGRA-VNKFltghftryvdYDFTARL---------EDDLDAVSRGEKEWIPLME 563

                         650       660       670       680       690
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1169100938 584 HTLDVFKRKFHYFVDSIAGMDELMEVSFSPLAATGKPLS-RCGkchRFMKYIQ 635
Cdd:PRK08780  564 KFWGPFKELVEEKKDSVDRTEAGQVRELGTDPKSGKPVSvRIG---RFGPMVQ 613
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 1-602 4.24e-23

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 105.81  E-value: 4.24e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTvLMVAEKPSLAQSIAKILS--RGSLSSHKglngacsvhEYtgtFAGQpvRFKMTSVCGHVMTL----DFLGKYNKWD 74
Cdd:PRK14724    1 TKT-LVIAEKPSVAQDIVRALTpvAGKFEKHD---------EH---FESD--SYVVTSAVGHLVEIqapeEFDVKRGKWS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  75 ----KVDPAElFSQAPTEKKEAnpKLNMVkFLQVEGRGCDYIVLWLDCDKEGENIcFEVLDAVlpVMNKAHGGEKTVFRA 150
Cdd:PRK14724   66 fanlPVIPPY-FDLKPVDKTKT--RLNAV-VKLAKRKDVTELVNACDAGREGELI-FRLIEQY--AGGAKGGLGKPVKRL 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 151 RFSSITDTDICNAMACLGEPDHNEALSVDAR--QELDLRIGCAFTRFQTKyFQGKYGDLdsSLISFGPCQTPTLGFCVER 228
Cdd:PRK14724  139 WLQSMTPQAIRDGFDNLRSDAQMQGLASAARsrSEADWLVGINGTRAMTA-FNSRDGGF--FLTTVGRVQTPTLSLVVER 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 229 HDKIQSFKPETYWVLQAKVNTDKDRSL--LLD--WDRV---------RVFDREIAQMFLNMTKlEKEAQVEATSrKEKAK 295
Cdd:PRK14724  216 EEKIRKFVSRDYWEIHAGFHAEAGEYLgkWFDpqWKKAsddpearadRVWSEREARAIADAVR-GKAATVTEES-KPTTQ 293

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 296 QRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ-GYISYPRTETTHYPEN--------FDL--KGSLRQQANHPYWA 364
Cdd:PRK14724  294 ASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDylpvakqtFEMlaTSGMRHLAPFAQQA 373

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 365 dtvkrlLAEGINRPRK----GHDAGDHPPITPMKSA----TEAElggdaWRLYEYITRHFIATVSHDCKYLQST-ISFRI 435
Cdd:PRK14724  374 ------LDGNYVRPSKrifdNSKVSDHFAIIPTTQApsglSEAE-----QKLYDLVVRRFMAVFFPSAEYQVTTrISQVV 442

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 436 GPElFTCSGKTVLSPGF---------TEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLME-- 504
Cdd:PRK14724  443 GHS-FKTEGKVLVKPGWlaiygkeaaNEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsa 521

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 505 --------------KHGIGTDASIPVHINNICQRNYVTVEsGRRLKPTNLGIVLVHGYYKIDA-ELVLPTIRSAVEKQLN 569
Cdd:PRK14724  522 gkqidddelreamqEKGLGTPATRAAIIEGLLTEKYMLRE-GRELIPTAKAFQLMTLLRGLGVeELSRAELTGEWEYKLA 600

                         650       660       670
                  ....*....|....*....|....*....|....*..
gi 1169100938 570 LIAQGK----ADYRQVLGHTLDVFKRKFHYFVDSIAG 602
Cdd:PRK14724  601 QMEKGQlsreAFMQQIAAMTEKLVKKAKEYDRDTIPG 637
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 1-589 4.02e-21

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 99.13  E-value: 4.02e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   1 MKTVLMVAEKPSLAQSIAKILSRGslsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTL-----------DFLGK 69
Cdd:PRK06319    1 MKKSLIIVESPAKIKTLQKLLGEG---------------------------FIFASSLGHIVDLpakefgidienDFEPD 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938  70 YnkwdkvdpaelfsQAPTEKKEanpklnMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDaVLPVMNKahggektVFR 149
Cdd:PRK06319   54 Y-------------QILPDKEE------VINKICKLAKKCDVVYLSPDPDREGEAIAWHIAN-QLPKNTK-------IQR 106

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 150 ARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGdldsslISFGPCQTPTLGFCVERH 229
Cdd:PRK06319  107 ISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSG------VSAGRVQSVALKLVVDRE 180

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 230 DKIQSFKPETYWVLQAKVNTDKDRSLLL---------DWDR-----------VRVFDREIAQMFLNMtkLEKEA-QVEAT 288
Cdd:PRK06319  181 KAIEAFVPVEYWNIRVHLKDPKTQKTFWahlysvdgkKWEKeipegktedevLLINSKEKADHIVEL--LESATyTVTRV 258

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 289 SRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLY---------TQGYISYPRTETTHY-PENFD-LKGSLRQQ 357
Cdd:PRK06319  259 ESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYegvdldsegATGLITYMRTDSVRTdPEALKqVRKYIEGT 338

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 358 ANHPYWADTVKRLLAEginrpRKGHDAgdHPPITPMKSATEAE-----LGGDAWRLYEYITRHFIATVSHDCKY--LQST 430
Cdd:PRK06319  339 FGKEFLPSSPNVYTTK-----KMAQDA--HEAIRPTDITLTPEklrskLTEDQYKLYSLIWKRFVASQMIPAIYdtLAIR 411

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 431 ISFRIGPELfTCSGKTVLSPGFTEV---MPWQSVPLEE--SLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEK 505
Cdd:PRK06319  412 ITTNKGIDL-RATGSLLKFKGFLAVyeeKRDDEGDEEEniHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEK 490

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 506 HGIGTDASIPVHINNICQRNYvTVESGRRLKPTNLGIVLVHGYykidaELVLPTI-----RSAVEKQLNLIAQGKADYRQ 580
Cdd:PRK06319  491 SGIGRPSTYATIMNKIQSREY-TLKENQRLRPTELGKIISQFL-----ETNFPRImdigfTALMEDELELIADNKKPWKL 564


                  ....*....
gi 1169100938 581 VLGHTLDVF 589
Cdd:PRK06319  565 LLQEFWELF 573
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 112-573 8.78e-12

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 69.20  E-value: 8.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 112 IVLWLDCDKEGENICFEVLDAVLPVMNKAhggeKTVF-RARFSSITDTDICNAMA--CLGEPDHNEALSVDARQELDlRI 188
Cdd:PTZ00407  128 IILATDPDREGELIAVHALQTIKRLYPKL----KVPFsRAYMHSITEDGIRKAMRerHVEACDYDLANAAETRHAMD-RI 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 189 gcaftrfqtkyfqgkYGDLDSSLI--------SFGPCQTPTLGFCVERHDKIQSF--KPETYWVLQA------------- 245
Cdd:PTZ00407  203 ---------------FGFLGSSVVraansqmrSIGRVQTPALILINEREDKIKAFleSNKSTFEVQAmcqfpsphgttfs 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 246 ---KVNTDKdRSLLLDWDRVRVFDREIAQMFLNMT---KLEKEAQVEATsrkEKAKQRPLALNTveMLRVASSSLGMGPQ 319
Cdd:PTZ00407  268 qvvTITPDR-KGGASHWATEAEARRCLEQWKLNNCtgfSVPLEPKPQPS---VVPPPQPFTMAT--AIAKANRQLKYSSE 341

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 320 HAMQTAERLYTQGYISYPRTETTHYPENF--DLKGSLRQQANhpywadtvKRLLAEGINRPRKGHDaGDHPPITPMKSAT 397
Cdd:PTZ00407  342 MVSGCLQDLFQLGHITYPRTDSTRIDESAlpDIYAAVKKEFG--------KEFLYRLEDRTVSAQE-GKGSKKTGKKRST 412

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 398 EAELGGDAWR------------------------------LYEYITRHFIAT--VSHDCKYLQSTISFRI--GPEL-FTC 442
Cdd:PTZ00407  413 KQKKGADTPVgnvedaheairptnidttgeslslspptraVYDLVRRNTLAVfmIPMKTEKIVATVKFTSgsGEKLeFEL 492

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 443 SGKTVLSPGFTE----------------------------VMPWQS-------VPLEESLPTCQRGDAFPVGEVKMLEKQ 487
Cdd:PTZ00407  493 QGKRVVEPGWTRafhkgdkgttgpaeetdeditaveegapVVPSLSqeefkaiMNLRSQLGSGVQKGFFELRSPQVRENR 572

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938 488 TNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHgyykiDAELVLPTI-----RS 562
Cdd:PTZ00407  573 PVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVE-----TAKSTFPSIvdigfTA 647

                         570
                  ....*....|.
gi 1169100938 563 AVEKQLNLIAQ 573
Cdd:PTZ00407  648 AFEKKLDRIAK 658
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 4-155 1.42e-10

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 58.52  E-value: 1.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938   4 VLMVAEKPSLAQSIAKILSRGSlsshkglngacsvheytgtfagqpvrFKMTSVCGHVMTLDFlgkynkwdkvdpaelfs 83
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGF--------------------------QAVVAVLGHLLSLEK----------------- 37

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1169100938  84 qaptekkeaNPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVmnkahggEKTVFRARFSSI 155
Cdd:pfam01751  38 ---------GPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL-------ENAGGRVEFSEL 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
4-137 1.04e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 1.04e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169100938    4 VLMVAEKPSLAQSIAKILSRgslsshkglngacsvheytgtfagqpvRFKMTSVCGHVMTLDflgkynkwdkvdpaelfs 83
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGK---------------------------RGNVVALGGHLLSKE------------------ 36

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1169100938   84 qaptekkeanpklnMVKFLQVEGRGCdYIVLWLDCDKEGENICFEVLDAVLPVM 137
Cdd:smart00493  37 --------------QIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH